|
| Status |
Public on Nov 12, 2020 |
| Title |
3_3-OHBcP: 3-hydroxybenzo[c]phenanthrene (3-OHBcP)-treated |
| Sample type |
RNA |
| |
|
| Source name |
zebrafish scales
|
| Organism |
Danio rerio |
| Characteristics |
tissue: scale
|
| Treatment protocol |
The scales were incubated at 15 °C for 6 h in Leibovitz's L-15 medium (Invitrogen, Grand Island, NY, USA) with benzo[c]phenanthrene (BcP: 1 nM) or 3-hydroxybenzo[c]phenanthrene (3-OHBcP: 1 nM).
|
| Growth protocol |
Scales were collected from zebrafish under anesthesia.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared from zebrafish scales using a total RNA isolation kit for fibrous tissue (Qiagen GmbH, Hilden, Germany) and treated with DNase I (RNase-Free DNase kit, Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >8.5 were considered acceptable.
|
| Label |
biotin
|
| Label protocol |
500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.
|
| Scan protocol |
The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).
|
| Description |
Scales were incubated with 3-OHBcP at 15°C for 6 h.
|
| Data processing |
GeneChip Analysis Suite (Expression Console)
|
| |
|
| Submission date |
Nov 11, 2020 |
| Last update date |
Nov 12, 2020 |
| Contact name |
Yoshiaki Tabuchi |
| E-mail(s) |
ytabu@cts.u-toyama.ac.jp
|
| Organization name |
University of Toyama
|
| Department |
Life Science Research Center
|
| Lab |
Division of Molecular Genetics Research
|
| Street address |
2630 Sugitani
|
| City |
Toyama |
| State/province |
Toyama |
| ZIP/Postal code |
930-0194 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE161253 |
Effects of polycyclic aromatic hydrocarbons on osteoclasts and osteoblasts in the scales of zebrafish |
|
